[obs] Joining DwC, OBOE, PO and PATO

[Hilmar Lapp]

On Oct 27, 2010, at 1:24 AM, Cam Webb wrote:

> this calls for the need for a more semantically formal set of DwC  
> terms, a fork to create a `Darwin SW' to stand alongside Darwin Core.

I think so, too. I think DwC as a controlled vocabulary for exchanging  
specimen and occurrence data in a more standard way has strings  
pulling at it in different directions than we care about for obtaining  
more formal semantics. That doesn't mean they can't be married at some  
point, but an effort that is free from the legacy usage requirements  
can probably make faster progress on the hairy process of nailing down  
the consensus semantics of the major concepts in this area.

I don't think the TDWG LSID vocs are a good start though - they strike  
me as a hodgepodge of properties that are largely free of explicit  
semantics.

> The formal acceptance of such a new standard would take a long  
> time.  What do you suggest doing in the meantime?

I don't think that a process of formal acceptance of a new standard  
needs to or should hold up using it. In fact, if we want to consider  
the induction of an ontology into the OBO Foundry as a "formal  
acceptance" in that particular community, documented usage by at least  
2 independent (from the ontology authors) groups is a requirement for  
such acceptance.

So I don't see any hindrances to moving ahead.

> I don't see how to demarcate the level of hierarchy in PATO where a  
> pato:Quality shifts from just a oboe:Characteristic to a combination  
> of oboe:Characteristic and oboe:Value.

We have this exact problem in Phenoscape when we want to infer  
characters (for a matrix view) from a collection of EQ statements. To  
address this, we have introduced 'attribute' and 'value' subset  
annotations ("slims") to PATO. Based on that, we have an algorithm  
that returns the attribute for a PATO term Q as the first term in the  
lineage from Q to the root that is in the 'attribute' slim. (This may  
be Q itself.)

However, as Chris points out, it might also be fair to view all of  
PATO as attributes (characteristics).

> I meant that the phenoscape terms (e.g. hasPhenotype) are not  
> available yet in RDF, AFAIK.

True. I'm copying Jim here - Jim, are we publishing the Phenoscape  
predicates in RDF somewhere, and if not, what is keeping us from doing  
so?

	-hilmar

-- 
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: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
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